Changeset 10600

Timestamp:

2019-01-28T21:07:57+01:00 (5 years ago)

Author:

nicolasmartin

Message:

Review inclusion of RELEASE_NOTES in the index and several changes in formatting

Location:

NEMO/trunk

Files:

• RELEASE_NOTES.rst (modified) (9 diffs)
• doc/rst/source/NEMO_guide.rst (modified) (2 diffs)
• doc/rst/source/conf.py (modified) (1 diff)

NEMO/trunk/RELEASE_NOTES.rst

@@ -2 +2 @@
 Release Notes
 *************
-
-.. contents::
-   :local:
 
 New sea-ice component SI3 (in place of LIMx)
@@ -10 +7 @@
 
 - Physics
+
   - Lateral melting
-  - Melt ponds: constant or :doi:`10.1175/JCLI-D-11-00078.1 <Holland et al. 2012>` formulation (and soon topographic melt ponds)
-  - Ice-atm. drags from :doi:`10.1029/2012JD017630 <Lupkes et al. 2012>` (depending on ice concentration) or :doi:`10.1002/2014JD022418 <Lupkes et al. 2015>` (depending on sea ice concentration and atm. stability)
-  - Landfast ice (:doi:`10.1002/2016JC012006 <Lemieux et al. 2016>`)
+  - Melt ponds: constant or :doi:`Holland et al. 2012<10.1175/JCLI-D-11-00078.1>` formulation (and soon topographic melt ponds)
+  - Ice-atm. drags from :doi:`Lupkes et al. 2012<10.1029/2012JD017630>` (depending on ice concentration) or :doi:`Lupkes et al. 2015<10.1002/2014JD022418>` (depending on sea ice concentration and atm. stability)
+  - Landfast ice (:doi:`Lemieux et al. 2016<10.1002/2016JC012006>`)
 
 - Numerics
+
   - Advection: Ultimate-Macho scheme
-  - Rheology: adaptive EVP (:doi:`10.1016/j.ocemod.2016.03.004 <Kimmritz et al. 2017>`)
+  - Rheology: adaptive EVP (:doi:`Kimmritz et al. 2017<10.1016/j.ocemod.2016.03.004>`)
   - Coupling interface: conductivity as surface forcing instead of heat fluxes (Met Office requirement)
-    
+
 - Performance: all thermodynamics in 1D and reduced mpp communications
-    
 - Usability (users & developers friendly)
-  - Comprehensive set of outputs (universal units and understandable names + includes cmip)
+
+  - Comprehensive set of outputs (universal units and understandable names + includes CMIP)
   - New architecture and namelist
   - All processes can be decoupled from each other (switch on/off)
@@ -44 +43 @@
 
 - Fix for tracer conservation with split explicit free surface
-- Bulk formulae : move to aerobulk package (:doi:`10.1175/JPO-D-16-0169.1 <Brodeau et al. 2016>`), i.e. NCAR, COARE and ECMWF bulk
-                  (remove Clio and MFS bulk)
+- Bulk formulae : move to aerobulk package (:doi:`Brodeau et al. 2016<10.1175/JPO-D-16-0169.1>`), i.e. NCAR, COARE and ECMWF bulk (remove Clio and MFS bulk)
 - Wetting and drying
 - Added tidal self attraction and loading either read from a file or from usual "scalar" approximation
@@ -52 +50 @@
 - iso-neutral mixing (iso and triad operators):
   add the Method of Stabilizing Correction (MSC) (more accurate calculation) + add a bilaplacian case
-- Lateral physics (LDF): scale aware setting of eddy viscosity and diffusivity
-- Vorticity: 2 new energy conserving scheme:
-  ENT with Coriolis defined at T-point (better for Flux form) and
-  EET a variant of EEN where e3t is used instead of e3f
-  (solved the issue with e3f specification but is not enstrophy conserving) 
+- Lateral physics (``LDF``): scale aware setting of eddy viscosity and diffusivity
+- Vorticity: 2 new energy conserving scheme: ENT with Coriolis defined at T-point (better for Flux form) and EET a variant of EEN where e3t is used instead of e3f (solved the issue with e3f specification but is not enstrophy conserving) 
 
 Test Cases
@@ -62 +57 @@
 
 The first test cases available for now are:
+
 - ``CANAL``: east-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex)
-- ``ICE_AGRIF``: east-west + north-south periodic channel. The common configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the key_agrif in the cpp keys.
-- ``ISOMIP``: simple box configuration with an ice shelf with simple geometry on top. The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. The exact original setup is described ​here.
-- ``LOCK-EXCHANGE``:classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. It has been used by several authors including Burchard and Bolding (2002) and Ilıcak et al. (2012). The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing
-- ``OVERFLOW``: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by Ilıcak et al. (2012)
-- ``VORTEX``: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. It is implemented here with an online refined subdomain (thanks to AGRIF library) out of which the vortex propagates. It serves as a benchmark to diagnose nesting errors as in Debreu et al. (2012), Penven et al. (2006) and Spall and Holland (1991)
-- ``WAD``: a set of simple closed basin geometries for testing the Wetting and drying capabilities. Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge. 
+- ``ICE_AGRIF``: east-west + north-south periodic channel. The common configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the ``key_agrif`` in the cpp keys
+- ``ISOMIP``: simple box configuration with an ice shelf with simple geometry on top. The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. The exact original setup is described ​here
+- ``LOCK-EXCHANGE``: classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. It has been used by several authors including Burchard and Bolding (2002) and :doi:`Ilıcak et al. (2012)<10.1016/j.ocemod.2011.10.003>`. The ``LOCK EXCHANGE`` experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing
+- ``OVERFLOW``: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by :doi:`Ilıcak et al. (2012)<10.1016/j.ocemod.2011.10.003>`
+- ``VORTEX``: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. It is implemented here with an online refined subdomain (thanks to ``AGRIF`` library) out of which the vortex propagates. It serves as a benchmark to diagnose nesting errors as in :doi:`Debreu et al. (2012)<10.1016/j.ocemod.2012.03.003>`, :doi:`Penven et al. (2006)<10.1016/j.ocemod.2005.05.002>` and :doi:`Spall and Holland (1991)<10.1175/1520-0485(1991)021<0205:ANPEMF>2.0.CO;2>`
+- ``WAD``: a set of simple closed basin geometries for testing the wetting and drying capabilities. Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge
 
 New Reference configurations
@@ -74 +70 @@
 
 ``AGRIF_DEMO``: 2 interlocked zooms (1:4 & 1:3) in the Nordic Seas + 1 zoom (1:1) at the equator
+
 ``SPITZ12``: regional configuration around the Svalbard archipelago 
 
@@ -80 +77 @@
 
 Coupled interface to external wave model
+
 Large scale wave interaction process added in momentum and tracer equations 
 
@@ -85 +83 @@
 =======================================================
 
-- The passive tracers transport component was redesigned toward a modular structure and users can enable each module directly through logical flags in namelist_top (no more fortran macros!).
-- :doc:`tracers <TOP on-line user documentation>`
-- ``TOP`` currently accounts for the following 5 modules:
-  ``CFC`` contains inorganic carbon tracers (CFC11/CFC12/SF6),
-  ``MY_TRC`` is a template for new modules (or external couplings),
-  ``AGE`` deals with water age tracking,
-  ``C14`` as a radiocarbon passive tracer, and
-  the companion ecosystem model ``PISCES``.
-- A generalized infrastructure was developed to handle the prescription of either surface, coastal, or open boundaries conditions for each passive tracer.
-- A new configuration, named ORCA2_OFF_TRC, was created to provide a benchmark simulation environment to deal with inert carbon tracers dynamics by exploiting the offline coupling with NEMO.
+- The passive tracers transport component was redesigned toward a modular structure and users can enable each module directly through logical flags in namelist_top (no more fortran macros!)
+- :doc:`TOP on-line user documentation<tracers>`
+- TOP currently accounts for the following 5 modules: ``CFC`` contains inorganic carbon tracers (CFC11/CFC12/SF6), ``MY_TRC`` is a template for new modules (or external couplings), ``AGE`` deals with water age tracking, ``C14`` as a radiocarbon passive tracer, and the companion ecosystem model ``PISCES``
+- A generalized infrastructure was developed to handle the prescription of either surface, coastal, or open boundaries conditions for each passive tracer
+- A new configuration, named ``ORCA2_OFF_TRC``, was created to provide a benchmark simulation environment to deal with inert carbon tracers dynamics by exploiting the offline coupling with NEMO
 - PISCES model contains new developments and modifications:
-  - Particulate Organic Carbon (POC) component comes with a new liability scheme, while the former Kriest parametrisation was superseded;
+
+  - Particulate Organic Carbon (POC) component comes with a new liability scheme, while the former Kriest parametrisation was superseded
   - A complex iron chemistry scheme is now available, with an improved description of ligands for the marine iron cycle
-  - Carbonate chemistry is based on MOCSY 2.0 routines (see :doi:`10.5194/gmd-8-485-2015 <Orr and Epitalon, 2015>`), by complying also with CMIP6 standards.
+  - Carbonate chemistry is based on MOCSY 2.0 routines (see :doi:`10.5194/gmd-8-485-2015 <Orr and Epitalon, 2015>`), by complying also with CMIP6 standards
   - Ecosystem components can be optionally modelled by means of explicit nutrient quotas (PISCES-QUOTA) 
 
@@ -106 +100 @@
 - Reduce number of MPI communications
   (suppression of redundant communications, gather multiple communications into one)
-- Use of MPI-3 asynchronous routines for performance (use key_mpi2 if MPI-3 not available)
+- Use of MPI-3 asynchronous routines for performance (use ``key_mpi2`` if MPI-3 not available)
 - Back to standard dynamical allocation (remove of wrk_alloc/dealloc statements)
-- :xios:`<XIOS software>` for IOs version 2.5 as default, and optionally available for restarts 
+- :xios:`XIOS software<>` for IOs version 2.5 as default, and optionally available for restarts 
 
 Simplification and robustness
 =============================
 
-- Revised structure of namelist_ref/_cfg and default reference values.
-- Lateral physics (LDF): simplification of user interface and removal of CPP keys
-- Vertical physics (ZDF) (modularity, share shear production calculation between TKE and GKS, removal of all ZDF CPP keys, removal of avmu & avmv, minimization of MPP comm.: ~15 removed)
-  Remove the split-explicit ZDF scheme for both TRA and DYN
-  Remove the acceleration of convergence
-  Generalised lbc_lnk and lbc_nfd
-  Unify mppini
-  Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns
-  MPI Message passing re coded
-  Configuration interface completely rewritten
-  (DOM module mainly suppressed , and in place: domain_cfg.nc file, or usr_def module) 
+- Revised structure of ``namelist_ref`` / ``namelist_cfg`` and default reference values
+- Lateral physics (``LDF``): simplification of user interface and removal of CPP keys
+- Vertical physics (``ZDF``) (modularity, share shear production calculation between TKE and GKS, removal of all ZDF CPP keys, removal of ``avmu`` & ``avmv``, minimization of MPP comm.: ~15 removed)
+- Remove the split-explicit ZDF scheme for both ``TRA`` and ``DYN``
+- Remove the acceleration of convergence
+- Generalised ``lbc_lnk`` and ``lbc_nfd``
+- Unify mppini
+- Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns
+- MPI Message passing re coded
+- Configuration interface completely rewritten (``DOM`` module mainly suppressed , and in place: ``domain_cfg.nc`` file, or ``usr_def`` module) 
 
 Collaborative Development Environment
 =====================================
 
-- Access to information on NEMO wiki reorganised through portals for users/developers/System Team and complete refactoring of all wiki pages and their layout
-- Reorganisation of SVN repository to be compliant with usual directory tree and facilitate building of NEMO executable
-- Define and install a separate repository for test cases to all easy contributions from the NEMO Users Community
-- :forge:`discussion <Forums>` created
-- ​:nemo:`<NEMO public web site>` has been cleaned and is now much nicer (using Wordpress instead of EzP)
+- Access to information on wiki reorganised through portals for users/developers/System Team and complete refactoring of all pages and their layout
+- Reorganisation of SVN repository to be compliant with usual directory tree and facilitate building of the executable
+- Define and install a separate repository for test cases to all easy contributions from the community
+- :forge:`Forums<discussion>` created
+- :website:`Public web site<>` has been revamped and cleaned using Wordpress
 - New mailing lists have been set up
 - Improvements of reliability through automatic and regular testing of the changes made in repository 

NEMO/trunk/doc/rst/source/NEMO_guide.rst

@@ -16 +16 @@
 
 .. toctree::
-   :hidden:
-   :caption: What's new in NEMO 4.0
+   :hidden:
 
-   release_notes
+   release_notes
 
 .. toctree::
-   :hidden:
-   :caption: Getting started
+   :hidden:
+   :caption: Getting started
 
-   install
-   configurations
-   test_cases
+   install
+   configurations
+   test_cases
 
 .. toctree::
-   :hidden:
-   :caption: Setup your configuration
+   :hidden:
+   :caption: Setup your configuration
 
-   setup
-   diagnostics
-   tools
+   setup
+   diagnostics
+   tools
 
 .. toctree::
-   :hidden:
-   :caption: Advanced use
+   :hidden:
+   :caption: Advanced use
 
-   zooms
-   coupling
-   data_assimilation
-   tracers
+   zooms
+   coupling
+   data_assimilation
+   tracers
 
 .. toctree::
-        :hidden:
-        :caption: Contributions are welcome!
+   :hidden:
+   :caption: Contributions are welcome!
 
-        contributing
+   contributing
 
 .. toctree::
-   :hidden:
-   :caption: Glossary
+   :hidden:
+   :caption: Glossary
 
-   definitions
+   definitions
 
 .. include:: readme.rst
@@ -65 +64 @@
 ======================
 
-.. bibliography:: references.bib
-   :all:
-   :style: unsrt
-   :labelprefix: R
+.. bibliography:: references.bib
+   :all:
+   :style: unsrt
+   :labelprefix: R
 
 Disclaimer

NEMO/trunk/doc/rst/source/conf.py

@@ -15 +15 @@
 version = '4.0'
 # The full version, including alpha/beta/rc tags
-release = '4.0'
+release = 'release-4.0'